decodegenetics / read_haps Goto Github PK

I am using a valid BAM file (many other tools are consuming it no problem). My VCF is also seemingly valid. Any thoughts on what might be going on here?

$ ~/projects/other_tools/read_haps/bin/read_haps GBA.aligned.deduped.sort.bam ~/projects/other_tools/read_haps/high_quality_markers_deCODE_2015.txt.gz ./GBA.octopus.vcf.gz -fa ~/wgs_resources/data/reference/human/human_g1k_v37_modified.fasta/human_g1k_v37_modified.fasta SNP_PAIRS ERROR_PAIRS DOUBLE_ERROR_PAIR_COUNT DOUBLE_ERROR_FRACTION REL_ERROR_FRACTION NONSENSE_FRACTION PASS_FAIL REASON 0 0 0 0 0 0 FAIL READ_PAIR_COUNT

Thanks-
john major

Hello,

I'm trying to test the software on some samples, but I only get the FAIL and READ_PAIR_COUNT for my tests. These samples (BAM and VCF) are definitely processed on hg38. It seems to fail instantaneously. Below is the command (full paths redacted):

[read_haps-0.2]$ ./read_haps -v -fa {redacted}/hg38.fa {redacted}/SL362490.bam {redacted}/read_haps/high_quality_markers_deCODE_2015.txt.gz {redacted}/SL362490.vcf.gz
parsed args 
read pos used file 
read VCF header 
SNP_PAIRS ERROR_PAIRS DOUBLE_ERROR_PAIR_COUNT DOUBLE_ERROR_FRACTION REL_ERROR_FRACTION NONSENSE_FRACTION PASS_FAIL REASON
0 0 0 0 0 0 FAIL READ_PAIR_COUNT
[read_haps-0.2]$ 

Thoughts on debugging the issue?